To investigate the sources and toxicity of metals in Bohai Sea sediments, concentration and geochemical speciation of metals of surface sediments were measured. Metal distributions and principal component analysis suggested that Zn, Pb, Cd, and Ag were largely derived from anthropogenic sources, whereas the majority of the other metals studied here were found to have been derived from natural rock weathering and calcareous marine biota. The major sources of anthropogenic metal inputs to the study region are from the mining industry, port transport services, vehicle exhausts, and agricultural runoff. Empirical sediment quality guidelines and the risk assessment code were used to evaluate the metal toxicities in this area. Our results show that Cd presents a high risk to the ecological system because it was found in the non-residual phase, which tends to be weakly bound and highly bioavailable; Cu, Pb, Ni, and Co pose a low risk; Zn and Cr present no risk. The use of the threshold effects level and effects range-low values of Cd and Cr as guidelines for the Bohai Sea are of limited use as they do not account for the bioavailability and toxicity of the elements in marine environments. Assessment of the annual metal fluxes from riverine and atmospheric sources indicates that the largest contributions of metals to the Bohai Sea were derived from the suspended particulate load of rivers. Furthermore, it was found that the main depositional zones for metals in the Bohai Sea were in estuaries and the center mud zones.